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<h1 class="epydoc">Source Code for <a href="scripts.ms_jsfs-module.html">Script scripts.ms_jsfs</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt>  <tt class="py-line"><tt class="py-comment">#!/usr/bin/env python</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt>  <tt class="py-line"><tt class="py-docstring">Convert ms output to a frequency spectrum.</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt>  <tt class="py-line"><tt class="py-docstring">Reads the ms results from stdin and outputs to stdout.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt>  <tt class="py-line"><tt class="py-docstring">If the '-av' flag is passed, the output is the average spectrum of the ms</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt>  <tt class="py-line"><tt class="py-docstring">iterations. Otherwise it is the sum.</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt>  <tt class="py-line"><tt class="py-docstring"></tt> </tt>
<a name="L10"></a><tt class="py-lineno">10</tt>  <tt class="py-line"><tt class="py-docstring">For example: 'ms &lt;details&gt; | ms_jsfs.py -av &gt; output.fs'</tt> </tt>
<a name="L11"></a><tt class="py-lineno">11</tt>  <tt class="py-line"><tt class="py-docstring">"""</tt> </tt>
<a name="L12"></a><tt class="py-lineno">12</tt>  <tt class="py-line"> </tt>
<a name="L13"></a><tt class="py-lineno">13</tt>  <tt class="py-line"><tt class="py-keyword">if</tt> <tt class="py-name">__name__</tt> <tt class="py-op">==</tt> <tt class="py-string">'__main__'</tt><tt class="py-op">:</tt> </tt>
<a name="L14"></a><tt class="py-lineno">14</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt class="py-name">sys</tt> </tt>
<a name="L15"></a><tt class="py-lineno">15</tt>  <tt class="py-line">    <tt class="py-keyword">import</tt> <tt id="link-0" class="py-name" targets="Package dadi=dadi-module.html"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-0', 'dadi', 'link-0');">dadi</a></tt> </tt>
<a name="L16"></a><tt class="py-lineno">16</tt>  <tt class="py-line"> </tt>
<a name="L17"></a><tt class="py-lineno">17</tt>  <tt class="py-line">    <tt class="py-name">average</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt class="py-string">'-av'</tt> <tt class="py-keyword">in</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">argv</tt><tt class="py-op">)</tt> </tt>
<a name="L18"></a><tt class="py-lineno">18</tt>  <tt class="py-line">     </tt>
<a name="L19"></a><tt class="py-lineno">19</tt>  <tt class="py-line">    <tt class="py-name">input</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdin</tt> </tt>
<a name="L20"></a><tt class="py-lineno">20</tt>  <tt class="py-line">    <tt class="py-name">output</tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">stdout</tt> </tt>
<a name="L21"></a><tt class="py-lineno">21</tt>  <tt class="py-line">    <tt class="py-name">sfs</tt><tt class="py-op">,</tt><tt class="py-name">header</tt> <tt class="py-op">=</tt> <tt id="link-1" class="py-name"><a title="dadi" class="py-name" href="#" onclick="return doclink('link-1', 'dadi', 'link-0');">dadi</a></tt><tt class="py-op">.</tt><tt id="link-2" class="py-name" targets="Variable dadi.Demographics1D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Variable dadi.Demographics2D.Spectrum=dadi.Spectrum_mod.Spectrum-class.html,Class dadi.Spectrum_mod.Spectrum=dadi.Spectrum_mod.Spectrum-class.html"><a title="dadi.Demographics1D.Spectrum
dadi.Demographics2D.Spectrum
dadi.Spectrum_mod.Spectrum" class="py-name" href="#" onclick="return doclink('link-2', 'Spectrum', 'link-2');">Spectrum</a></tt><tt class="py-op">.</tt><tt id="link-3" class="py-name" targets="Static Method dadi.Spectrum_mod.Spectrum.from_ms_file()=dadi.Spectrum_mod.Spectrum-class.html#from_ms_file"><a title="dadi.Spectrum_mod.Spectrum.from_ms_file" class="py-name" href="#" onclick="return doclink('link-3', 'from_ms_file', 'link-3');">from_ms_file</a></tt><tt class="py-op">(</tt><tt class="py-name">input</tt><tt class="py-op">,</tt> <tt class="py-name">average</tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.mask_corners()=dadi.Spectrum_mod.Spectrum-class.html#mask_corners"><a title="dadi.Spectrum_mod.Spectrum.mask_corners" class="py-name" href="#" onclick="return doclink('link-4', 'mask_corners', 'link-4');">mask_corners</a></tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">,</tt> </tt>
<a name="L22"></a><tt class="py-lineno">22</tt>  <tt class="py-line">                                            <tt class="py-name">return_header</tt><tt class="py-op">=</tt><tt class="py-name">True</tt><tt class="py-op">)</tt> </tt>
<a name="L23"></a><tt class="py-lineno">23</tt>  <tt class="py-line">     </tt>
<a name="L24"></a><tt class="py-lineno">24</tt>  <tt class="py-line">    <tt class="py-name">sfs</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name" targets="Method dadi.Spectrum_mod.Spectrum.to_file()=dadi.Spectrum_mod.Spectrum-class.html#to_file"><a title="dadi.Spectrum_mod.Spectrum.to_file" class="py-name" href="#" onclick="return doclink('link-5', 'to_file', 'link-5');">to_file</a></tt><tt class="py-op">(</tt><tt class="py-name">output</tt><tt class="py-op">,</tt> <tt class="py-name">comment_lines</tt><tt class="py-op">=</tt><tt class="py-name">header</tt><tt class="py-op">)</tt> </tt>
<a name="L25"></a><tt class="py-lineno">25</tt>  <tt class="py-line"> </tt><script type="text/javascript">
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</pre>
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